[gmx-developers] (no subject)SGIweirdness
ksr at chemistry.umass.edu
Thu Jun 16 21:36:12 CEST 2005
Sorry about omitting the subject line.
The system is a simple temperature unfolding, single protein in water
I'll let you know what we find.
On Jun 16, 2005, at 3:30 PM, David wrote:
> On Thu, 2005-06-16 at 14:48 -0400, Ken Rotondi wrote:
>> Dear Gromacs community,
>> Well, it appears we've stumbled across some genuine weirdness here.
>> CVS version of GROMACS runs on our SGI supercomputer:
>> SGI Origin 3800, 128 processor R14000 500 MHz
>> SGI Message Passing Toolkit 1.6 (this is SGI's tuned MPI libraries)
>> FFTW version 2.1.3 (single-precision, shared libraries, MPI-enabled)
>> The issue is, it won't run on more than 24 processors without
>> generating an MPI error, which may be an issue with GROMACS or an
>> with something on the SGI.
> What kind of system are you testing?
>> This is the error message when it dies using more than 24 processors:
>> MPI: MPI_COMM_WORLD rank 0 has terminated without calling
>> MPI: Received signal 10
> This is a USR1 signal, which is very weird, because it can only be
> issued by the user. Have you checked md0.log, since processor 0 appears
> to be the culprit.
> #define SIGUSR1 10 /* User-defined signal 1 (POSIX). */
> You can also try mdrun -debug (if you have enough disk space)...
>> It dumps a nasty core file which doesn't contain usable symbols (We
>> probably need to recompile without stripping the binaries). I've
>> noticed that it also takes a long time to set up before dying compared
>> to the set up and successful run using 24 processors.
>> Sorry to post to both developers and users, but I thought it might be
>> CVS issue.
>> Thanks for any insight/help,
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org
> gmx-developers mailing list
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